Structure and Self-Assembly of Biomolecules through Molecular Simulations

In the field of bio-inspired materials, the non-covalent self-assembly of relatively simple peptide based molecules has gained increasing attention for the formation of biologically functional materials, all with nanoscale order. Self-assembly is often associated with human medical disorders. Our work concerns the modeling of small biological molecules, such as peptides and lipids as well as of proteins, where the self-assembly propensity and the conformational properties, are studied through all-atom Molecular Dynamics simulations in explicit solvent. Of particular interest is diphenylalanine (FF) peptide, the study of which reveals a strong self-assembling propensity in water in contrast to its behavior in methanol. Furthermore, a systematic comparison in the self-assembly features among dipeptides in aqueous solutions which belong to two different classes “Val-Ala” (Alanine-Isoleucine and Isoleucine-Isoleucine) and “Phe-Phe” (FF), has been performed. A clearly stronger attraction is observed between Phe-Phe dipeptides. Our results are in qualitative agreement with experimental observations. Conformational properties of proteins in aqueous solution, are also studied, in terms of their structural stability and their thermosensitivity and possible mutations are explored.